Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A3 F1 I1 R1
|
57 |
49.8 |
2216334 |
94.8% |
2101084 |
113.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,649,905 |
G→A |
P795S (CCG→TCG) |
yfhM ← |
bacterial alpha2‑macroglobulin colonization factor ECAM, anti‑host protease defense factor, periplasmic inner membrane‑anchored lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,649,905 | 0 | G | A | 95.3%
| 130.8
/ ‑6.1
| 43 | P795S (CCG→TCG) | yfhM | bacterial alpha2‑macroglobulin colonization factor ECAM, anti‑host protease defense factor, periplasmic inner membrane‑anchored lipoprotein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (26/15); minor base C (0/2); total (26/17) |
| Fisher's exact test for biased strand distribution p-value = 1.51e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGGAGCGAGATTTATCGCCAGGACGTACCACCAGCGTACTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAACTGGCTTTATCCAGTTTCAGCGTGACACGGTCGGGTCGCACTGC > NC_000913/2649773‑2650034
|
cgGAGCGAGATTTATCGCCAGGACGTACCACCAGCGTACTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCAGAGCGACCCTTc > 1:717050/1‑139 (MQ=255)
aTTTATCGCCAGGACGTACCACCAGCGTACTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTc < 2:762106/139‑1 (MQ=255)
tATCGCCAGGACGTACCACCAGCGTACTTAAACACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAc < 2:907246/139‑1 (MQ=255)
gACGTACCACCAGCGTACTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGAcc < 1:230254/114‑1 (MQ=255)
gACGTACCACCAGCGTACTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGAcc > 2:230254/1‑114 (MQ=255)
gACGTACCACCAGCGTACTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAc < 2:853230/130‑1 (MQ=255)
gACGTACCACCAGCGTACTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAc > 1:853230/1‑130 (MQ=255)
cGTACTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACccgcc > 2:26227/1‑139 (MQ=255)
cTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTg > 1:730290/1‑139 (MQ=255)
aaaTACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGCCCCTTCACTGGACTCGACCATCGCATAACCTTTCCCCGCCGTTGgcg < 1:26227/139‑1 (MQ=255)
aGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGgcgcagc > 2:663085/1‑134 (MQ=255)
aGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCgcagc < 1:663085/137‑1 (MQ=255)
aTCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACTGCGACCCTTCACTGGACTCCACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGata > 2:911103/1‑139 (MQ=255)
aTCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCAc > 1:496740/1‑92 (MQ=255)
aTCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCAc < 2:496740/92‑1 (MQ=255)
aTCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGata > 2:887412/1‑139 (MQ=255)
aTCATGACGAATCGAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCGACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGata > 2:740538/1‑139 (MQ=255)
cATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATg > 1:622762/1‑139 (MQ=255)
cATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATg < 1:887412/139‑1 (MQ=255)
cATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTGGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACGGAACTCGACCATCGCAAAACTTTTACCCGCCGTTGGCGCGGCGATATg < 2:717050/139‑1 (MQ=255)
gACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCGCTTGAGCCCGAACATCGATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAcc < 2:729947/98‑1 (MQ=255)
gACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAcc < 2:60191/98‑1 (MQ=255)
gACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAcc > 1:729947/1‑98 (MQ=255)
gACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGAcc > 1:60191/1‑98 (MQ=255)
gACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCaa > 1:838817/1‑139 (MQ=255)
ttCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCATCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTaa > 2:753550/1‑139 (MQ=255)
taGGTTTTTCCGACAGGAATCGTCAGATCCAGCCTTTGAGCCCGAACATCAACATCTCGCCCCCACAGCGACCCTTCACTTGACCCGACCATCGCATACCTTGCGCCCGCCGTTGGCGCGGCGATATGCAACTTAATgg < 2:565487/138‑1 (MQ=255)
aGGTTTTATCGACCGGAATGGTCAGATCCACCCCTTGAGCCCGAACATCAACCTCTTGCCCCCACAGCGCCCTTTCGCTGGACTCGACCATCGCATACCCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGgt < 2:724104/139‑1 (MQ=255)
tATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGcc > 1:724104/1‑139 (MQ=255)
tCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAACTGGc > 1:307977/1‑139 (MQ=255)
cAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAACTGGCt > 1:646961/1‑139 (MQ=255)
tCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCgcgg > 2:392465/1‑94 (MQ=255)
tCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCgcgg < 1:392465/94‑1 (MQ=255)
cccTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTAcc > 1:779222/1‑75 (MQ=255)
cccTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAACTGGCTTTATCCAGt < 1:97652/139‑1 (MQ=255)
cccTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACGGGACTCGACCATCGCATAACCTTTAcc < 2:779222/75‑1 (MQ=255)
aGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACccgccaacg < 2:95158/77‑5 (MQ=255)
aGCCCGAACATCAATCTCTTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACccgccaacg > 1:95158/1‑73 (MQ=255)
ctTGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAACTGGCTTTATCCAGTTTCAGCGTGACACggtcgggtcg > 1:251535/1‑139 (MQ=255)
tGCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAACTGGCTTTATCCAGTTTCAGCGTGACACGGTCGGGTCGCa > 1:127899/1‑139 (MQ=255)
gCCACCACAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAACTGGCTTTATCCAGTTTCAGCGTGACACGGTCGGGTCGCAc > 1:770239/1‑139 (MQ=255)
ccaccaCAGCGACCCTTCACTGGACTCGACCATCGCa < 2:386460/37‑1 (MQ=255)
ccaccaCAGCGACCCTTCACTGGACTCGACCATCGCa > 1:386460/1‑37 (MQ=255)
accacAGCGACCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAACTGGCTTTATCCAGTTTCAGCGTGACACGGTCGGGTCGCACTgc > 1:67131/1‑139 (MQ=255)
|
CGGAGCGAGATTTATCGCCAGGACGTACCACCAGCGTACTTAAATACAGATCATGACGATTCCAGGTTTTATCGACCGGAATCGTCAGATCCAGCCCTTGAGCCCGAACATCAATCTCTTGCCACCACAGCGGCCCTTCACTGGACTCGACCATCGCATAACCTTTACCCGCCGTTGGCGCGGCGATATGCAACTTAATGGTGTCGCCAGGGCGATAACTGGCTTTATCCAGTTTCAGCGTGACACGGTCGGGTCGCACTGC > NC_000913/2649773‑2650034
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
